qPCR results from Plates 1 and 2 from DNA (2ul) from 1/2 of the 0.45um water filters from FHL 2026 experiment.
Experiment details:
Experiment info: Lab Notebook Post
Plate 1 Samples Run:
Protocol notes:
See document here: qPCR Notes Plate 1, tab for Plate 1, July 23, 2026.
qPCR run results:
| qPCR run results - FHL 2026 water filter plate 1 | |
|---|---|
| R^2 | 0.995 |
| y-int | 36.879 |
| Slope | -3.411 |
| E | 96.4% |
Results files: here
Plate 2 Samples Run:
Protocol Notes:
See document here: qPCR Notes Plate 2, tab for Plate 2, July 24, 2026.
qPCR run results:
| qPCR run results - FHL 2026 water filter plate 2 | unfiltered | remove D3 (one of the reps of a standard curve) from analysis |
|---|---|---|
| R^2 | 0.85 | 0.979 |
| y-int | 37.296 | 36.393 |
| Slope | -3.358 | -3.266 |
| E | 98.50% | 102.50% |
Results files: here
Filtered results: here
Plates 1 and 2 Results Figure:
Very rough, created in excel to show what’s going on (spreadsheet here).
Y-axis is the mean starting quantity across the replicates for each sample. qPCR is targeting V. pecenicida.
X-axis is the sample ID. Sample IDs all start with “F” for “Filter”. Then a series of letters that correspond to the treatment group, and then a number for the sample number (treamtent replicate).
The codes for the treatments are:
| code | treatment |
|---|---|
| Blank | DNA Extraction blank (control) |
| EM | Eelgrass + mussels + seawater + culture media |
| EMVP | Eelgrass + mussels + seawater + V. pec |
| MSW | Mussel + seawter + culture media |
| MVP | Mussel + seawater + V. pec |
| ShSW | Mussel shell + seawter + culture media |
| SW | seawter + culture media |
| T0 | time point zero: seawater + V. pec |
| VPSW | V. pec + seawater |
There’s still about 2 more plates worth of samples to run (one plate: 24 samples; second plate: final 8 samples + 16 eelgrass swab DNA).
So I will run the third plate next Tuesday, then I’ll extract DNA from a batch of eelgrass swabs and then run the final filter plate + some of the eelgrass swab DNA afterwards.
Assessing Supplies and Things I need to order:
I have:
- 8 qPCR plates
- tons of tubes
- tons of qPCR plate adhesive films
- enough 10um F and R primers diluted for 8 more plates (and 100um F and R primers to dilute for more)
- enough 10um Probe diluted for ~7 more plates (and 100um of Probe to dilute for more)
- tons of molecular grade water
- lots of serially diluted standard curve and more V. pectenicida to dilute more if needed
- tons of 1X buffer TE
- tons of BSA
- enough TaqMan Master Mix for ~3 more plates (NEED TO ORDER MORE)
- NEED TO ORDER MORE 10X EXO IPC MIX
- NEED TO ORDER MORE 50X EXO IPC DNA
Number of plates I need to run to finish all the remaining samples (after I extract DNA):
| sample types | DNA sample number | |
|---|---|---|
| 2026 filters | 80 | 75 samples + 5 blanks |
| eelgrass swab | 34 | 32 samples + 2 blanks |
| 2026 mussel tissue | 34 | 32 samples + 2 blanks |
| mussel swabs | 42 | 40 samples + 2 blanks |
| qPCR plate number | samples | sample type | status |
|---|---|---|---|
| Plate 1 | 24 | 2026 filters | DONE |
| Plate 2 | 24 | 2026 filters | DONE |
| Plate 3 | 24 | 2026 filters | |
| Plate 4 | 8 | 2026 water filters | |
| Plate 4 | 16 | eelgrass swabs | |
| Plate 5 | 18 | eelgrass swabs | |
| Plate 5 | 6 | mussel tissue | |
| Plate 6 | 24 | mussel tissue | |
| Plate 7 | 4 | mussel tissue | |
| Plate 7 | 20 | mussel swabs | |
| Plate 8 | 22 | mussel swabs |
SO!!!!
I will need to run at least 6 more qPCR plates (I say at least because the above numbers assume I don’t need to re-run any plates).
Therefore, I definitely need to order:
- more TaqMan Master Mix
- More 10X EXO IPC MIX
- More 50X EXO IPC DNA
I’ll hold off on ordering more plates because as it is I have 2 extra, so I may not need more.